I think the question is answered rather easily (if not satisfyingly) by making the fair assumption that the writers just kept pulling villains out of their asses.

It's clear the Fallen didn't exist before the second movie. It's also rather strange that no one mentioned Transformers being found in the 1960's in the first two movies. You would think that would have come up at some point. They didn't plan anything out for the franchise. It's just bad writing.

Sector 7 & the U.S. Government were keeping secrets from each other for decades.

__________________"Welcome To The Worst Nightmare Of All Reality.""Maybe Things In Their Life Were Going Wrong & They Just Needed Someone To Take Their Spite Out On."